Evidence for a high pK_a of an aspartic acid residue in the active site of CALB by a fully atomistic multiscale approach

Abstract

Candida antarctica Lipase B (CALB) is a paradigm for the family of lipases. At pH 7, the optimal pH for catalysis, the protonation state of an aspartic acid of the active site (Asp134) could not be conclusively assigned. In fact, the pK_a estimate provided by a widely used computational tool, namely PropKa, that predicts pKa values of ionizable groups in proteins based on the crystallographic structure, is only slightly above 7 (pKa = 7.25). This, along with the lack of an experimental evaluation, makes the assignment of its protonation state at neutral pH challenging. Here, we calculate the pK_a of Asp134 by means of a fully atomistic multiscale computational approach based on classical molecular dynamics (MD) simulation and the perturbed matrix method (PMM), namely the MD-PMM approach. MD-PMM is able to take into account the dynamics of the system and, at the same time, to treat the deprotonation step at the quantum level. The calculations provide a pK_a value of 8.9 ± 1.1, hence suggesting that Asp134 in CALB should be protonated at neutral, and even at slightly basic, pH.

Communicated by Ramaswamy H. Sarma

Keywords:

• Candida antarctica lipase B
• perturbed matrix method
• molecular dynamics simulations
• hybrid quantum-classical approach
• pKa calculation

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

CINECA infrastructures via IscraC project (HP10CY92M3) provided the computational hours for the calculations.